Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites.

Details

Serval ID
serval:BIB_C0A73F212EB6
Type
Article: article from journal or magazin.
Collection
Publications
Title
Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites.
Journal
Journal of Molecular Biology
Author(s)
Roulet E., Bucher P., Schneider R., Wingender E., Dusserre Y., Werner T., Mermod N.
ISSN
0022-2836[print], 0022-2836[linking]
Publication state
Published
Issued date
2000
Volume
297
Number
4
Pages
833-848
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Abstract
Accurate prediction of transcription factor binding sites is needed to unravel the function and regulation of genes discovered in genome sequencing projects. To evaluate current computer prediction tools, we have begun a systematic study of the sequence-specific DNA-binding of a transcription factor belonging to the CTF/NFI family. Using a systematic collection of rationally designed oligonucleotides combined with an in vitro DNA binding assay, we found that the sequence specificity of this protein cannot be represented by a simple consensus sequence or weight matrix. For instance, CTF/NFI uses a flexible DNA binding mode that allows for variations of the binding site length. From the experimental data, we derived a novel prediction method using a generalised profile as a binding site predictor. Experimental evaluation of the generalised profile indicated that it accurately predicts the binding affinity of the transcription factor to natural or synthetic DNA sequences. Furthermore, the in vitro measured binding affinities of a subset of oligonucleotides were found to correlate with their transcriptional activities in transfected cells. The combined computational-experimental approach exemplified in this work thus resulted in an accurate prediction method for CTF/NFI binding sites potentially functioning as regulatory regions in vivo.
Keywords
Adenoviruses, Human/genetics, Algorithms, Base Sequence, Binding Sites, CCAAT-Enhancer-Binding Proteins, Cell Line, Computer Simulation, Consensus Sequence/genetics, DNA/genetics, DNA/metabolism, DNA-Binding Proteins/metabolism, Dimerization, Humans, Mutation/genetics, NFI Transcription Factors, Oligodeoxyribonucleotides/chemistry, Oligodeoxyribonucleotides/genetics, Promoter Regions, Genetic/genetics, Replication Origin/genetics, Reproducibility of Results, Response Elements/genetics, Substrate Specificity, Thermodynamics, Transcription Factors/metabolism, Transcriptional Activation/genetics, Transfection
Pubmed
Web of science
Create date
24/01/2008 11:41
Last modification date
20/08/2019 16:35
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